I've just tried it on an epub in the iBooks app on my iPad (both of which are up-to-date) and I can scroll down the list of bookmarks. Holding the iPad in portrait mode 11 are viewable on the screen at a time, but I can scroll up and down the list by using a finger in the middle of the screen - you aren't trying to scroll via the left or right hand margin ?
Now I understand just what my problem was. I'll explain for the benefit of anyone who might still have trouble scrolling after reading the solution.
I was placing my finger on the *bottom* margin of the page and trying to scroll up (to see the lower part of the list). The trick is to place your finger on the list itself, not the white space below.